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Released as 20141122 ('Rosetta').
This commit is contained in:
Ole Tange
parent
763dd12caa
commit
2c9971729b
35
NEWS
35
NEWS
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@ -1,3 +1,38 @@
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20141122
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* Remote systems can be divided into hostgroups (e.g. web and db) by
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prepending '@groupname/' to the sshlogin. Multiple groups can be
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given by separating groups with '+'. E.g. @web/www1 @web+db/www2
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@db/mariadb
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* Remote execution can be restricted to servers that are part of one
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or more groups by '@groupname' as an sshlogin. Multiple groups can
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be given by separating groups with '+'. E.g. -S @web or -S @db+web
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* With --hostgroup you can restrict arguments to certain hostgroups by
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appending '@groupname' to the argument. Multiple groups can be
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given by separating groups with '+'. E.g. my_web_arg@web
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db-or-web-arg@db+web db-only-arg@db Thanks to Michel Courtine for
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developing a prototype for this.
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* HTSeq-Hadoop: Extending HTSeq for Massively Parallel Sequencing Data
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Analysis using Hadoop
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http://essenceofescience.se/wp-content/uploads/2014/11/Siretskiy.pdf
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* GNU Parallel was cited in: SlideToolkit: An Assistive Toolset for
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the Histological Quantification of Whole Slide Images
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http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0110289#close
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* GNU Parallel was cited in: Exploring a multiprocessor design space
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to analyze the impact of using STT-RAM in the memory hierarchy
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http://conservancy.umn.edu/bitstream/handle/11299/167286/Borse_umn_0130M_15431.pdf
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* Command-Line OCR with Tesseract on Mac OS X
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https://ryanfb.github.io/etc/2014/11/13/command_line_ocr_on_mac_os_x.html
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* Bug fixes and man page updates.
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20141022
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* --env was changed to deal with Bash's new way of exporting a function.
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12
README
12
README
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@ -40,9 +40,9 @@ document.
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Full installation of GNU Parallel is as simple as:
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wget http://ftpmirror.gnu.org/parallel/parallel-20141022.tar.bz2
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bzip2 -dc parallel-20141022.tar.bz2 | tar xvf -
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cd parallel-20141022
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wget http://ftpmirror.gnu.org/parallel/parallel-20141122.tar.bz2
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bzip2 -dc parallel-20141122.tar.bz2 | tar xvf -
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cd parallel-20141122
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./configure && make && make install
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@ -51,9 +51,9 @@ Full installation of GNU Parallel is as simple as:
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If you are not root you can add ~/bin to your path and install in
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~/bin and ~/share:
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wget http://ftpmirror.gnu.org/parallel/parallel-20141022.tar.bz2
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bzip2 -dc parallel-20141022.tar.bz2 | tar xvf -
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cd parallel-20141022
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wget http://ftpmirror.gnu.org/parallel/parallel-20141122.tar.bz2
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bzip2 -dc parallel-20141122.tar.bz2 | tar xvf -
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cd parallel-20141122
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./configure --prefix=$HOME && make && make install
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Or if your system lacks 'make' you can simply copy src/parallel
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20
configure
vendored
20
configure
vendored
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@ -1,6 +1,6 @@
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#! /bin/sh
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# Guess values for system-dependent variables and create Makefiles.
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# Generated by GNU Autoconf 2.69 for parallel 20141022.
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# Generated by GNU Autoconf 2.69 for parallel 20141122.
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#
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# Report bugs to <bug-parallel@gnu.org>.
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#
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@ -579,8 +579,8 @@ MAKEFLAGS=
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# Identity of this package.
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PACKAGE_NAME='parallel'
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PACKAGE_TARNAME='parallel'
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PACKAGE_VERSION='20141022'
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PACKAGE_STRING='parallel 20141022'
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PACKAGE_VERSION='20141122'
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PACKAGE_STRING='parallel 20141122'
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PACKAGE_BUGREPORT='bug-parallel@gnu.org'
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PACKAGE_URL=''
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@ -1203,7 +1203,7 @@ if test "$ac_init_help" = "long"; then
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# Omit some internal or obsolete options to make the list less imposing.
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# This message is too long to be a string in the A/UX 3.1 sh.
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cat <<_ACEOF
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\`configure' configures parallel 20141022 to adapt to many kinds of systems.
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\`configure' configures parallel 20141122 to adapt to many kinds of systems.
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Usage: $0 [OPTION]... [VAR=VALUE]...
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@ -1269,7 +1269,7 @@ fi
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if test -n "$ac_init_help"; then
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case $ac_init_help in
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short | recursive ) echo "Configuration of parallel 20141022:";;
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short | recursive ) echo "Configuration of parallel 20141122:";;
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esac
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cat <<\_ACEOF
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@ -1345,7 +1345,7 @@ fi
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test -n "$ac_init_help" && exit $ac_status
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if $ac_init_version; then
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cat <<\_ACEOF
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parallel configure 20141022
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parallel configure 20141122
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generated by GNU Autoconf 2.69
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Copyright (C) 2012 Free Software Foundation, Inc.
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@ -1362,7 +1362,7 @@ cat >config.log <<_ACEOF
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This file contains any messages produced by compilers while
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running configure, to aid debugging if configure makes a mistake.
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It was created by parallel $as_me 20141022, which was
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It was created by parallel $as_me 20141122, which was
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generated by GNU Autoconf 2.69. Invocation command line was
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$ $0 $@
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@ -2225,7 +2225,7 @@ fi
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# Define the identity of the package.
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PACKAGE='parallel'
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VERSION='20141022'
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VERSION='20141122'
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cat >>confdefs.h <<_ACEOF
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@ -2867,7 +2867,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
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# report actual input values of CONFIG_FILES etc. instead of their
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# values after options handling.
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ac_log="
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This file was extended by parallel $as_me 20141022, which was
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This file was extended by parallel $as_me 20141122, which was
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generated by GNU Autoconf 2.69. Invocation command line was
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CONFIG_FILES = $CONFIG_FILES
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@ -2929,7 +2929,7 @@ _ACEOF
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cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
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ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
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ac_cs_version="\\
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parallel config.status 20141022
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parallel config.status 20141122
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configured by $0, generated by GNU Autoconf 2.69,
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with options \\"\$ac_cs_config\\"
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@ -1,4 +1,4 @@
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AC_INIT([parallel], [20141022], [bug-parallel@gnu.org])
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AC_INIT([parallel], [20141122], [bug-parallel@gnu.org])
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AM_INIT_AUTOMAKE([-Wall -Werror foreign])
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AC_CONFIG_HEADERS([config.h])
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AC_CONFIG_FILES([
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@ -232,7 +232,10 @@ GNU Parallel 20141122 ('Rosetta') has been released. It is available for downloa
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Haiku of the month:
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<<>>
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Hadoop bit too much?
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Want a simpler syntax now?
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Use GNU Parallel.
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-- Ole Tange
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A central piece of command generation was rewritten making this release beta quality. As always it passes the testsuite, so most functionality clearly works.
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@ -244,6 +247,8 @@ New in this release:
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* With --hostgroup you can restrict arguments to certain hostgroups by appending '@groupname' to the argument. Multiple groups can be given by separating groups with '+'. E.g. my_web_arg@web db-or-web-arg@db+web db-only-arg@db Thanks to Michel Courtine for developing a prototype for this.
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* HTSeq-Hadoop: Extending HTSeq for Massively Parallel Sequencing Data Analysis using Hadoop http://essenceofescience.se/wp-content/uploads/2014/11/Siretskiy.pdf
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* GNU Parallel was cited in: SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0110289#close
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* GNU Parallel was cited in: Exploring a multiprocessor design space to analyze the impact of using STT-RAM in the memory hierarchy http://conservancy.umn.edu/bitstream/handle/11299/167286/Borse_umn_0130M_15431.pdf
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@ -1,6 +1,6 @@
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Summary: Shell tool for executing jobs in parallel
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Name: parallel
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Version: 20141022
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Version: 20141122
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Release: 1
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License: GPL
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Group: Productivity/File utilities
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@ -24,7 +24,7 @@
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use strict;
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use Getopt::Long;
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$Global::progname="niceload";
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$Global::version = 20141023;
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$Global::version = 20141122;
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Getopt::Long::Configure("bundling","require_order");
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get_options_from_array(\@ARGV) || die_usage();
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if($opt::version) {
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26
src/parallel
26
src/parallel
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@ -507,8 +507,6 @@ sub nindex {
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}
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$sleep = ::reap_usleep($sleep);
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}
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# TODO Why is needed?
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# start_more_jobs();
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return $something_written;
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}
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}
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@ -783,7 +781,7 @@ sub get_options_from_array {
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sub parse_options {
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# Returns: N/A
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# Defaults:
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$Global::version = 20141111;
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$Global::version = 20141122;
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$Global::progname = 'parallel';
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$Global::infinity = 2**31;
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$Global::debug = 0;
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@ -5159,6 +5157,17 @@ sub write {
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}
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sub set_stdin_buffer {
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# Copy stdin buffer from $block_ref up to $endpos
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# Prepend with $header_ref
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# Remove $recstart and $recend if needed
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# Input:
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# $header_ref = ref to $header to prepend
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# $block_ref = ref to $block to pass on
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# $endpos = length of $block to pass on
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# $recstart = --recstart regexp
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# $recend = --recend regexp
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# Returns:
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# N/A
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my $self = shift;
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my ($header_ref,$block_ref,$endpos,$recstart,$recend) = @_;
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$self->{'stdin_buffer'} = ($self->virgin() ? $$header_ref : "").substr($$block_ref,0,$endpos);
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# * not mixing STDERR and STDOUT
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# * terminating with ctrl-c
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# It works on Linux but not Solaris
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# Finishes on Solaris, but wrong exit code:
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# $SIG{CHLD} = sub {exit ($?&127 ? 128+($?&127) : 1+$?>>8)};
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# Hangs on Solaris, but correct exit code on Linux:
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# $SIG{CHLD} = sub { $done = 1 };
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# $p->poll;
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my $signal_script = "perl -e '".
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q{
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use IO::Poll;
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$SIG{CHLD} = sub {exit ($?&127 ? 128+($?&127) : 1+$?>>8)};
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$SIG{CHLD} = sub { $done = 1 };
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$p = IO::Poll->new;
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$p->mask(STDOUT, POLLHUP);
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$pid=fork; unless($pid) {setpgrp; exec $ENV{SHELL}, "-c", @ARGV; die "exec: $!\n"}
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$p->poll;
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$p->poll;
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kill SIGHUP, -${pid} unless $done;
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wait; exit ($?&127 ? 128+($?&127) : 1+$?>>8)
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} . "' ";
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($pre
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. "$sshcmd $ssh_options $serverlogin $parallel_env "
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. $remote_pre
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# . ::shell_quote_scalar($signal_script . ::shell_quote_scalar($next_command_line))
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# . ::shell_quote_scalar($signal_script . ::shell_quote_scalar($command))
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. ::shell_quote_scalar($command)
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. ";"
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. $post);
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@ -2373,6 +2373,27 @@ can be written like this:
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cat list | parallel "do_something {} scale {.}.jpg ; do_step2 <{} {.}" |\
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process_output
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If the body of the loop is bigger, it improves readability to use a function:
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(for x in `cat list` ; do
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do_something $x
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[... 100 lines that do something with $x ...]
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done) | process_output
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cat list | (while read x ; do
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do_something $x
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[... 100 lines that do something with $x ...]
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done) | process_output
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can both be rewritten as:
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doit() {
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x=$1
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do_something $x
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[... 100 lines that do something with $x ...]
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}
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export -f doit
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cat list | parallel doit
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=head1 EXAMPLE: Rewriting nested for-loops
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2
src/sql
2
src/sql
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@ -566,7 +566,7 @@ $Global::Initfile && unlink $Global::Initfile;
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exit ($err);
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sub parse_options {
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$Global::version = 20141023;
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$Global::version = 20141122;
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$Global::progname = 'sql';
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# This must be done first as this may exec myself
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@ -1,7 +1,7 @@
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#!/bin/bash
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# force load > 10
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while uptime | grep -v age:.[1-9][0-9].[0-9][0-9] >/dev/null ; do (timeout 5 nice burnP6 2>/dev/null &) done
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while uptime | grep -v age:.[1-9]\\+[0-9].[0-9][0-9] >/dev/null ; do (timeout 5 nice burnP6 2>/dev/null &) done
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int() {
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perl -pe 's/(\d+\.\d*)/int($1)/e'
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